EVA: A Novel Theoretical Descriptor for QSAR Studies

Perspectives in Drug Discovery and Design

Volumn 9--11, Issue , 1998, Pages 381-398

  Heritage, Trevor W ^a   Ferguson, Allan M ^a   Turner, David B ^b   Willett, Peter ^b  

^a TRIPOS INC   (United States)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001824196     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (37)

1. Hansch, C. and Fujilta, T., P-σ-π analysis: A method for the correlation of biological activity and chemical structure, J. Am. Chem. Soc., 86 (1964) 1616-1626.
2. Wiese, M., In Kubinyi, H. (Ed.) 3D QSAR in drug design, ESCOM, Leiden, 1993.
3. Cramer, R.D., Patterson, D.E. and Bunce, J.D. Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 110 (1988) 5959-5967.
4. Kim, K.H. and Martin, Y.C., Direct prediction of linear free-energy substituent effects from 3D structures using comparative molecular-field analysis: 1. Electronic effects of substituted benzoic-acids, J. Org. Chem., 56 (1991) 2723-2729.
5. Klebe, G., Abraham, U. and Mietzner, T., Molecular similarity indexes in a comparative-analysis (CoMSIA) of drug molecules to correlate and predict their biological activity, J. Med. Chem., 37 (1994) 4130-4146.
6. Kellogg, G.E., Semus, S.F. and Abraham, D.J., HINT-A new method of empirical hydrophobic field calculation for CoMFA, J. Comput.-Aided Mol. Design, 5 (1991) 545-552.
7. Good, A.C., The calculation of molecular similarity: Alternative formulas, data manipulation and graphical display, J. Mol. Graph., 10 (1992) 144-151.
8. Good, A.C., Hodgkin, E.E. and Richards, W.G., The utilisation of Gaussian functions for the rapid evaluation of molecular similarity, J. Chem. Inf. Comput. Sci., 32 (1992) 188-191.
9. Thorner, D.A., Wild, D.J., Willett, P. and Wright, P.M., Similarity searching in files of three-dimensional structures: Flexible field-based searching of MEP, J. Chem. Inf. Comput. Sci., 36 (1996) 900-908.
10. Wagener, M., Sadowski, J. and Gasteiger, J., Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic Ah receptor activity by neural networks, J. Am. Chem. Soc., 117 (1995) 7769-7775.
11. Silvennan, B.D. and Platt, DE., Comparative molecular moment analysis (CoMMA): 3D QSAK without molecular superposition, J. Med. Chem., 39 (1996) 2129-2140.
12. Clementi, S., Cruciani, G., Riganelli, D. and Valigi, R., In Dean, P.M., Jolies, G. and Newton, C.G. (Eds.) New perspectives in drug design. Academic Press, London, 1995, pp. 285-310.
13. Ferguson, A .M. and Heritage, T .W., Shell Research Ltd. Internal Report, 1990 (not publicly available).
14. Herzberg, G., Molecular Spectra and Molecular Structure: II. Infrared and Raman Spectra Polyatomic Molecules, 8th Ed., D. Van Nostrrand Company Inc., New York, 1945.
15. Ferguson, A.M., and Jonathan, P., Shell Research Ltd. Internal Report, 1990 (not publicly available).
16. Lindberg, W., Persson, J.-A. and Wolds, S., Partial least-squares method for spectrofluorimetric analysis of mixtures of humic acid and ligninsulfonate, Anal. Chem., 55 (1983) 643-648.
17. Waszkowycz, B., Clark, D.E., Frenkel, D., Li, J., Murray, C.W., Robson, B. and Westhead, D.R., PROG-LIGAND-an approach to de Novo molecular design: 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores, J. Med. Chem., 37 (1994) 3994-4002.
18. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, Jr., S. and Weiner, P., A novel force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc., 106 (1984) 765-784.
19. Ferguson, A.M., Heritage, T.W., Jonathan, P., Pack, S.E., Phillips, L., Rogan, J. and Snaith, P.J., EVA: A new theoretically based molecular descriptor for use in QSAK/QSPR analysis. J. Comput.-Aided Mol. Design, 11 (1997) 143-152.
20. Cramer III, R.D., BC (DEF) Parameters: 1. The intrinsic dimensionality of intermolecular interactions in the liquid state, J. Am. Chem. Soc., 102(1980) 1837-1849.
21. Stewart, J.J.P., Optimisation of Parameters for Semiempirical Methods: 2. Applications, J. Comp. Chem., 10 (1989) 221-264.
22. Stewart, J.J.P., MOPAC: A semiempirical molecular orbital program, J. Comput.-Aided Mol. Design, 4 (1990) 1-105.
23. Turner, D.B., Willett, P., Ferguson, A.M. and Heritage, T.W., Evaluation of a novel infra-red range vibration-based descriptor (EVA) for QSAR studies: 1. General application, J. Comput.-Aided Mol. Design, 11 (1997) 409-422.
24. Turner, D.B., An Evaluation of a novel molecular descriptor (EVA) for QSAR studies and the similarity searching of chemical structure databases, PhD. thesis, University of Sheffield, 1996.
25. Jonathan, P., McCarthy, W.V. and Roberts, A.M.I., Discriminant analysis with singular covariance matrices: A method incorporating crossvalidation and efficient randomized permutation tests. J. Chemometrics, 10 (1996) 189-214.
26. Waller, C.L. and McKinney, J.D., Comparative molecular field analysis of polyhalogenated dibenzo-p-dioxins, dibenzofurans and biphenyls, J. Med. Chem., 35 (1992) 2660-3666.
27. Carroll, F.I., Gao, Y.G., Rahman, M.A., Abraham, P., Parham, K., Lewin, A.H., Boja, J.W. and Kuhar, M.J., Synthesis, ligand-binding, QSAR, and CoMFA study of 3-β-(para-substituted phenyl)tropane-2-β-carboxylic acid methyl-esters, J. Med. Chem., 34 (1991) 2719-2725.
28. Allen, M.S., Laloggia, A.J., Dorn, L.J., Martin, M.J., Costantin, G., Hagen, T.J., Koehler, K.F., Skolnick, P. and Cook, J.M., Predictive binding of β-carboline inverse agonists and antagonists via the CoMFA/GOLPE approach, J. Med. Chem., 35 (1992) 4001-4010.
29. Greco, G., Novellino, E., Silipo, C. and Vittoria, A., Comparative molecular-field analysis on aset of muscarinic agonists, Quant. Struct.-Act. Relat., 10 (1991) 289-299.
30. 2-guided region selection for comparative molecular field-analysis: A simple method to achieve consistent results, J. Med. Chem., 38 (1995)1060-1066.
31. Turner, D.B., Willett, P., Ferguson, A.M. and Heritage, T.W., Evaluation of a novel infra-red range vibration-based descriptor (EVA) for QSAR studies: 2. Model validation, J. Med. Chem. (submitted).
32. Kroemer, R.T. and Hecht, P., Replacement of steric 6-12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency, J. Comput.-Aided Mol. Design, 9 (1995) 205-212.
33. Heritage, T.W., Shell Research Ltd. Internal Report, 1992 (not publicly available).
34. Wold, S., Johansson, E. and Cocchi, M., PLS-partial least squares to latent structures, In Kubinyi, H. (Ed.) 3D QSAR in drug design, ESCOM, Leiden, 1993, pp. 523-550.
35. Mickelson, K.E., Forsthoefel, J. and Westphal, U., Steroid-protein interactions: Human corticosteroid binding globulin: Some physicochemical properties and binding specificity, Biochemistry, 20 (1981) 6211-6218.
36. Ginn, C.M.R., Turner, D.B., Willett, P., Ferguson, A.M. and Heritage, T.W., Similarity searching in files of three-dimensional chemical structures: Evaluation of the EVA descriptor and combination of rankings using data fusion, J. Chem. Inf. Comput. Sci, 37 (1997) 23-37.
37. Dunn, W.J., Hopfinger, A.J., Catana, C. and Duraiswami, C., Solution of the conformation and alignment tensors for the binding of trimethoprim and its analogs to dihydrofolate-reductase -3D-quantitative structure-activity study using molecular-shape analysis, 3-way partial least-squares regression, and 3-way factor analysis, J. Med. Chem., 39 (1996) 4825-4832.